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- PDB-4m9d: The Crystal structure of an adenylosuccinate synthetase from Baci... -

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Basic information

Entry
Database: PDB / ID: 4m9d
TitleThe Crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor in complex with AMP.
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FORMIC ACID / MALONATE ION / PHOSPHATE ION / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.821 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The Crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor in complex with AMP.
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,56017
Polymers95,9542
Non-polymers1,60615
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-4 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.045, 255.947, 61.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-793-

HOH

21B-683-

HOH

DetailsThe chains A and B form a dimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate synthase / AMPSase / AdSS / IMP--aspartate ligase


Mass: 47977.211 Da / Num. of mol.: 2 / Mutation: Y370C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS5320, BA_5716, GBAA_5716, purA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81JI9, adenylosuccinate synthase

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Non-polymers , 6 types, 580 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Sodium Malonate, 12% (w/v) PEG 3350, 15mM AMP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.82→36 Å / Num. all: 90138 / Num. obs: 90138 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 6.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.2
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4510 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M0G

4m0g


Resolution: 1.821→35.5 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 4516 5.01 %Random
Rwork0.1532 ---
all0.1546 90104 --
obs0.1546 90104 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 105 565 7236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076826
X-RAY DIFFRACTIONf_angle_d1.0719251
X-RAY DIFFRACTIONf_dihedral_angle_d13.0212508
X-RAY DIFFRACTIONf_chiral_restr0.0721044
X-RAY DIFFRACTIONf_plane_restr0.0051205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8207-1.84140.25541660.21532711X-RAY DIFFRACTION97
1.8414-1.86310.22781500.19472855X-RAY DIFFRACTION100
1.8631-1.88580.22681590.19732760X-RAY DIFFRACTION100
1.8858-1.90960.23081570.19162856X-RAY DIFFRACTION100
1.9096-1.93480.24651470.18692791X-RAY DIFFRACTION100
1.9348-1.96130.23411740.1852814X-RAY DIFFRACTION100
1.9613-1.98930.23091620.17812829X-RAY DIFFRACTION100
1.9893-2.0190.19881320.16742830X-RAY DIFFRACTION100
2.019-2.05050.21751620.1632817X-RAY DIFFRACTION100
2.0505-2.08410.20851410.1552825X-RAY DIFFRACTION100
2.0841-2.12010.19361550.15482823X-RAY DIFFRACTION100
2.1201-2.15860.19091470.15252881X-RAY DIFFRACTION100
2.1586-2.20010.18751640.15212809X-RAY DIFFRACTION100
2.2001-2.2450.18351360.14982834X-RAY DIFFRACTION100
2.245-2.29380.17751210.14692862X-RAY DIFFRACTION100
2.2938-2.34720.17951570.15032858X-RAY DIFFRACTION100
2.3472-2.40590.19291320.15432836X-RAY DIFFRACTION100
2.4059-2.47090.2091350.15152874X-RAY DIFFRACTION100
2.4709-2.54360.18851530.1532858X-RAY DIFFRACTION100
2.5436-2.62570.19161310.15632865X-RAY DIFFRACTION100
2.6257-2.71950.18921410.1552865X-RAY DIFFRACTION100
2.7195-2.82830.2131390.16052863X-RAY DIFFRACTION100
2.8283-2.9570.20411490.16632865X-RAY DIFFRACTION100
2.957-3.11280.21531560.16292877X-RAY DIFFRACTION100
3.1128-3.30770.19251540.16552878X-RAY DIFFRACTION100
3.3077-3.56290.16621590.15712868X-RAY DIFFRACTION100
3.5629-3.9210.14231560.13052886X-RAY DIFFRACTION100
3.921-4.48740.14371550.12282910X-RAY DIFFRACTION100
4.4874-5.650.13811620.13662939X-RAY DIFFRACTION100
5.65-35.50630.18021640.15693049X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6137-0.12980.12541.2568-0.60891.47770.0655-0.12820.23540.3125-0.089-0.0355-0.40260.10330.01930.2521-0.04750.02440.1785-0.03480.197341.2896104.806236.9614
20.9953-0.0725-0.11071.1441-0.17771.05010.0298-0.1503-0.02110.1038-0.0169-0.05510.01570.1237-0.00670.1582-0.0281-0.00790.1851-0.01130.161143.822889.523632.1066
31.25940.2458-0.25232.86610.5480.9605-0.02310.12570.1755-0.34180.0896-0.17-0.21110.0016-0.06920.2453-0.01840.05110.15720.00690.205744.7934114.62613.9872
41.32250.13360.02260.58950.24131.4861-0.06670.13130.0075-0.06910.01780.1527-0.0354-0.20640.03920.15230.001-0.00240.1676-0.00080.170121.229483.031910.6549
51.1343-0.1762-0.14241.00810.13250.9655-0.02890.0726-0.036-0.10140.0238-0.08090.04710.10260.00990.1469-0.01390.01170.1531-0.0150.155738.719380.425813.334
61.0050.5675-0.24431.239-0.74450.79290.0039-0.0092-0.0334-0.02370.05860.09550.0177-0.0584-0.070.14240.00370.01110.1644-0.00920.151318.620178.535929.6162
72.67920.48041.08270.70520.08731.30860.0461-0.1840.01680.0672-0.03280.0644-0.1232-0.1697-0.01210.1750.01980.04180.19190.00210.189.231181.025934.5782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 423 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 230 )
6X-RAY DIFFRACTION6chain 'B' and (resid 231 through 338 )
7X-RAY DIFFRACTION7chain 'B' and (resid 339 through 428 )

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